def convertInputStep(self, movId, partId, postId):
inputMovies = self.inputMovies.get()
inputParts = self.inputParticles.get()
imgStar = self._getFileName('input_particles')
inputPartsFolder = self._getInputPath('particles')
pwutils.makePath(inputPartsFolder)
self.info("Converting set from '%s' into '%s'" %
(inputParts.getFileName(), imgStar))
tableGeneral = Table(columns=[
'rlnImageSizeX', 'rlnImageSizeY', 'rlnImageSizeZ',
'rlnMicrographMovieName', 'rlnMicrographBinning',
'rlnMicrographOriginalPixelSize', 'rlnMicrographDoseRate',
'rlnMicrographPreExposure', 'rlnVoltage',
'rlnMicrographStartFrame', 'rlnMotionModelVersion',
'rlnMicrographGainName', 'rlnMicrographDefectFile'
])
tableShifts = Table(columns=[
'rlnMicrographFrameNumber', 'rlnMicrographShiftX',
'rlnMicrographShiftY'
])
tableCoeffs = Table(
columns=['rlnMotionModelCoeffsIdx', 'rlnMotionModelCoeff'])
# Create the first row, later only the movieName will be updated
xdim, ydim, ndim = inputMovies.getDim()
acq = inputMovies.getAcquisition()
firstMovie = inputMovies.getFirstItem()
a0, aN = firstMovie.getAlignment().getRange()
moviesPixelSize = inputMovies.getSamplingRate()
binningFactor = inputParts.getSamplingRate() / moviesPixelSize
og = convert.OpticsGroups.fromImages(inputMovies)
writer = convert.createWriter(optics=og)
writer.writeSetOfMicrographs(inputMovies,
self._getFileName('input_mics'),
postprocessImageRow=self._updateMic)
tableGeneral.addRow(xdim, ydim, ndim, 'movieName',
binningFactor, moviesPixelSize,
acq.getDosePerFrame(), acq.getDoseInitial(),
acq.getVoltage(), a0, 0, '""', '""')
row = tableGeneral[0]
for movie in inputMovies:
movieStar = self._getMovieStar(movie)
ogId = movie.getAttributeValue('_rlnOpticsGroup', 1)
gainFn = og[ogId].get('rlnMicrographGainName', None)
defectFn = og[ogId].get('rlnMicrographDefectFile', None)
with open(movieStar, 'w') as f:
coeffs = json.loads(
movie.getAttributeValue('_rlnMotionModelCoeff', '[]'))
motionMode = 1 if coeffs else 0
# Update some params in the general table
replaceDict = {
'rlnMicrographMovieName': movie.getFileName(),
'rlnMotionModelVersion': motionMode
}
if gainFn:
replaceDict['rlnMicrographGainName'] = gainFn
if defectFn:
replaceDict['rlnMicrographDefectFile'] = defectFn
tableGeneral[0] = row._replace(**replaceDict)
tableGeneral.writeStar(f, tableName='general', singleRow=True)
# Write shifts
tableShifts.clearRows()
alignment = movie.getAlignment()
shiftsX, shiftsY = alignment.getShifts()
a0, aN = alignment.getRange()
empty = -9999.000
for i in range(1, a0):
tableShifts.addRow(i, empty, empty)
# Adjust the shifts to be relative to the first frame
# so let's add the opposite value
xoff, yoff = -shiftsX[0], -shiftsY[0]
for i in range(a0, aN + 1):
tableShifts.addRow(i, shiftsX[i - a0] + xoff,
shiftsY[i - a0] + yoff)
for i in range(aN + 1, ndim + 1):
tableShifts.addRow(i, empty, empty)
tableShifts.writeStar(f, tableName='global_shift')
# Write coefficients
tableCoeffs.clearRows()
if coeffs:
for i, c in enumerate(coeffs):
tableCoeffs.addRow(i, c)
tableCoeffs.writeStar(f, tableName='local_motion_model')
convert.writeSetOfParticles(inputParts,
imgStar,
outputDir=inputPartsFolder,
alignType=ALIGN_PROJ,
fillMagnification=True)
def convertInputStep(self, movId, partId, postId):
inputMovies = self.inputMovies.get()
inputParts = self.inputParticles.get()
imgStar = self._getPath('input_particles.star')
inputPartsFolder = self._getInputPath('particles')
pwutils.makePath(inputPartsFolder)
self.info("Converting set from '%s' into '%s'" %
(inputParts.getFileName(), imgStar))
tableMovies = Table(
columns=['rlnMicrographName', 'rlnMicrographMetadata'])
tableGeneral = Table(columns=[
'rlnImageSizeX', 'rlnImageSizeY', 'rlnImageSizeZ',
'rlnMicrographMovieName', 'rlnMicrographBinning',
'rlnMicrographOriginalPixelSize', 'rlnMicrographDoseRate',
'rlnMicrographPreExposure', 'rlnVoltage',
'rlnMicrographStartFrame', 'rlnMotionModelVersion'
])
tableShifts = Table(columns=[
'rlnMicrographFrameNumber', 'rlnMicrographShiftX',
'rlnMicrographShiftY'
])
tableCoeffs = Table(
columns=['rlnMotionModelCoeffsIdx', 'rlnMotionModelCoeff'])
# Create the first row, later only the movieName will be updated
xdim, ydim, ndim = inputMovies.getDim()
acq = inputMovies.getAcquisition()
firstMovie = inputMovies.getFirstItem()
a0, aN = firstMovie.getAlignment().getRange()
moviesPixelSize = inputMovies.getSamplingRate()
binningFactor = inputParts.getSamplingRate() / moviesPixelSize
hasLocal = firstMovie.hasAttribute('_rlnMotionModelCoeff')
motionMode = 1 if hasLocal else 0
tableGeneral.addRow(xdim, ydim, ndim, 'movieName',
binningFactor, moviesPixelSize,
acq.getDosePerFrame(), acq.getDoseInitial(),
acq.getVoltage(), a0, motionMode)
row = tableGeneral[0]
for movie in inputMovies:
movieFn = movie.getFileName()
movieBase = os.path.basename(movieFn)
movieStar = self._getInputPath(
pwutils.replaceBaseExt(movieFn, 'star'))
tableMovies.addRow(movieBase, movieStar)
with open(movieStar, 'w') as f:
# Update Movie name
tableGeneral[0] = row._replace(rlnMicrographMovieName=movieFn)
tableGeneral.writeStar(f, tableName='general', singleRow=True)
# Write shifts
tableShifts.clearRows()
alignment = movie.getAlignment()
shiftsX, shiftsY = alignment.getShifts()
a0, aN = alignment.getRange()
empty = -9999.000
for i in range(1, a0):
tableShifts.addRow(i, empty, empty)
# Adjust the shifts to be relative to the first frame
# so let's add the opposite value
xoff, yoff = -shiftsX[0], -shiftsY[0]
for i in range(a0, aN + 1):
tableShifts.addRow(i, shiftsX[i - a0] + xoff,
shiftsY[i - a0] + yoff)
for i in range(aN + 1, ndim + 1):
tableShifts.addRow(i, empty, empty)
tableShifts.writeStar(f, tableName='global_shift')
# Write coefficients
if hasLocal:
coeffs = movie.getAttributeValue('_rlnMotionModelCoeff',
'')
tableCoeffs.clearRows()
for i, c in enumerate(json.loads(coeffs)):
tableCoeffs.addRow(i, c)
tableCoeffs.writeStar(f, tableName='local_motion_model')
with open(self._getPath('input_corrected_micrographs.star'), 'w') as f:
tableMovies.writeStar(f)
convert.writeSetOfParticles(inputParts,
imgStar,
outputDir=inputPartsFolder,
alignType=ALIGN_PROJ,
fillMagnification=True)
